Are vertex groups that had Mask Modifiers applied to them gone forever?
Once you apply a modifier the transformation is permanent.



Modifiers are designed to work in a non-destructive way, once you apply them it is going to be very hard to go back to a previous state, as the undo function is quite limited (and completely unavailable once you save and re-open a project). 

Unless you have a good reason to apply a modifier, you don't need to

Form the blender Manual:


  Modifiers are automatic operations that affect an object in a non-destructive way. With modifiers, you can perform many effects automatically that would otherwise be too tedious to do manually (such as subdivision surfaces) and without affecting the base geometry of your object.
  
  They work by changing how an object is displayed and rendered, but not the geometry which you can edit directly. You can add several modifiers to a single object to form The Modifier Stack and Apply a modifier if you wish to make its changes permanent.


If you need to disable the modifier temporarily you can use the camera and eye icons.



Again, from the manual:


  Render (camera icon)
  
  Toggles visibility of the modifier’s effect in the render.
  
  Show in viewport (eye icon)
  
  Toggles visibility of the modifier’s effect in the 3D View.
  
  Show in Edit Mode (box icon)
  
  Displays the modified geometry in Edit Mode, as well as the original geometry which you can edit.
  
  Show on cage (triangle icon)
  
  When enabled, the final modified geometry will be shown in Edit Mode and can be edited directly.